structural-variation
There are 138 repositories under structural-variation topic.
fritzsedlazeck/Sniffles
Structural variation caller using third generation sequencing
dellytools/delly
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Illumina/manta
Structural variant and indel caller for mapped sequencing data
ACEnglish/truvari
Structural variant toolkit for VCFs
tjiangHIT/cuteSV
Long read based human genomic structural variation detection with cuteSV
brentp/smoove
structural variant calling and genotyping with existing tools, but, smoothly.
suhrig/arriba
Fast and accurate gene fusion detection from RNA-Seq data
broadinstitute/gatk-sv
A structural variation pipeline for short-read sequencing
cgroza/GraffiTE
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
Illumina/paragraph
Graph realignment tools for structural variants
hall-lab/svtools
Tools for processing and analyzing structural variants.
nanoporetech/pipeline-structural-variation
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
kcleal/dysgu
Toolkit for calling structural variants using short or long reads
brentp/duphold
don't get DUP'ed or DEL'ed by your putative SVs.
yjx1217/simuG
simuG: a general-purpose genome simulator
bioinformatics-centre/BayesTyper
A method for variant graph genotyping based on exact alignment of k-mers
sbslee/pypgx
A Python package for pharmacogenomics (PGx) research
bcgsc/mavis
Merging, Annotation, Validation, and Illustration of Structural variants
KCCG/ClinSV
Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
FunGeST/Palimpsest
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
XiaoTaoWang/NeoLoopFinder
A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
iprada/Circle-Map
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
SAMtoBAM/MUMandCo
MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation
murphycj/AGFusion
Python package to annotate and visualize gene fusions.
PacificBiosciences/sawfish
Joint structural variant and copy number variant caller for HiFi sequencing data
dantaki/SV2
Support Vector Structural Variation Genotyper
hall-lab/sv-pipeline
Pipeline for structural variation detection in cohorts
ITBE-Lab/MA
The Modular Aligner and The Modular SV Caller
mehrdadbakhtiari/adVNTR
A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
Kingsford-Group/squid
SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
akcorut/kGWASflow
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
Oshlack/MINTIE
Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.
kehrlab/PopDel
Population-wide Deletion Calling
Illumina/witty.er
What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
smehringer/SViper
Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.